The 71 to 29 per cent no-vote ensures the bitter industrial stalemate at the revenue agency, which is reeling from a disastrous IT crash this week, will drag on well into 2017.

Commissioner of Taxation Chris Jordan, who had campaigned hard for a yes-vote, told his workforce of the result on Wednesday afternoon after polls closed at 2pm.

"I had wanted to give you the news of a pay rise prior to the Christmas break, but with today's outcome I am disappointed that I am unable to do so," Mr Jordan wrote.

"I am sorry this is not a better outcome for all of us just before the holidays.

"I acknowledge this entire process has been going on for a very long time and I am not able to compensate for that.

"There are no options for back pay or bonuses to make up for the time without a pay rise."

Mr Jordan reiterated his point that he and other public service bosses were tightly constrained by government policy in what they could offer their workers.

"We continue to operate under a workplace bargaining policy that does not allow for these things," Mr Jordan wrote.

The main workplace union, the CSPU, said the result deepened the Tax Office's woes.

"We've had double confirmation this week of the real damage the Turnbull Government has done to the Tax Office, first with what was an unprecedented failure of the agency's critical systems and now with yet another enterprise agreement No vote," CPSU National Secretary Nadine Flood.

"The Turnbull Government has made illogical and short-sighted cuts to Tax."

The smaller Australian Services Union said the result was a reaction to a "poor offer".

"The strong no-vote was in response to Commissioner Jordan blaming the government and the Public Service Commissioner for his poor offer in April 2016 and now saying this last improved offer was also the best he could do," union official Jeff Lapidos said.